When is a Clone not a Clone?: The Danielle Codex
by Xenopsyche
Summary: A compilation of transcripts, documents, voice memos, security footage and other sources that detail Vlad's creation of Danielle and all the details and rationale behind it. Part of my 'Pre-emptive Strike' continuity.
1. Conceptualisation

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: I have been promising this one for a while, and now that 'The Events that Shape Us' is effectively complete, I have the perfect opportunity.**

**The entire point of this little story is to provide some background into Danielle's creation (in my head-canon), particularly the biology of it.**

**If you have read my other stories, then you will know that I consider her to be the biological daughter of Danny and Sam, rather than a straight clone (you just don't get a female by cloning a male unless something got _seriously_ messed up somewhere along the way).**

**And a note on Vlad; to my mind, he's a Psychopath, pure and simple, and his behaviour in these little snapshots reflect this. If he comes off as cold, fixated on his goal and devoid of Empathy, then that means I've done what I set out to do.**

**Thanks for taking the time to read and I hope you enjoy the chapter./AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 1: Conceptualisation**

* * *

******08/14/2004**

**Audio Transcript****, ****_Vladimir Masters _**

Clone 3, the first one to successfully complete the treatment regimen for the accelerated aging process, was another failure.

While his cells contained the ectoplasmic micro-cores of a Halfa, he seemed unable to utilise them. I will terminate and try again, with more ectoplasm in the growth-chamber this time.

* * *

******12/10/2004**

**Audio Transcript****, ****_Vladimir Masters _**

Clone 4 showed the same result. Minor physiological abnormalities aside, he is unable to utilise any of his spectral capabilities.

Even intense emotional factors such as fear were unable to trigger any effects.

I must be missing something….

* * *

******08/18/2004**

**Audio Transcript, ****_Vladimir Masters _**

In hindsight it is so simple…

The Primary Core, the one that Daniel and I would have received during our respective 'incidents' with that bumbling oaf Jack's lack of attention to detail-

*Deep Breath*

Jack's incompetence is not the issue here though; the point is that I now know why the previous clones have been unable to manifest any of the powers they should have had.

I will need to imbue them with a Primary Core in some… hmm, the most direct way would be to recreate the conditions of the accidents and expose them to an electric stimulus in a high ectoplasm environment, perhaps the growth chambers would suffice…

* * *

******12/21/2004**

**Audio Transcript****, ****_Vladimir Masters _**

It appears that the process of creating a Core is quite simple, but it does result in other… complications.

Clone 4 suffered extreme and rapid destabilisation of his ectoplasmic cores while attempting to complete my training course.

He had the misfortune to be in his ghost state at the time and was pulled apart at the cellular level.

I will try a different balance of current and ectoplasm with the next clone.

* * *

******12/21/2004**

**Security Footage, Camera 8 – Training Room: **

*The Clone (HF 04) enters the open training area in his human form*

Vlad:_ "__Good, you can follow basic instructions. Now transform."_

*HF 04 transforms, with noticeable difficulty*

Vlad:_"__Very good, now become invisible."_

*HF 04 disappears from view after 5 seconds of concentration*

Vlad:_"__Now intangibility."_

*HF 04 reappears, and appears to be intangible. A baseball is fired towards and through him.*

Vlad:_"__Hit the targets."_

*Three targets drop down from the ceiling and HF 04 hits all three with ectoblasts.*

Vlad:_"__Hmm, sloppy, but sufficient for now. Can you fly?"_

*HF 04 floats into the air in response.*

Vlad:_"__Now evade."_

*An automated ecto-gun begins firing rounds at HF 04, of which the first two are dodged, but the third impacts him.*

Vlad:_"__Embarrassing…very well, you are done for today, return to the growth chamber."_

*HF 04 has sunk to his knees and does not respond.*

Vlad:_"__Clone 4, I ordered you to-"_

* HF 04 begins to destabilise, emitting a scream as his body falls apart.*

Vlad:_"__Hmm, what an unexpected development; how unpleasant."_

* * *

******12/21/2004**

**Preliminary Autopsy Report: **

**Name/Designation:** HF 04

**Sex: **Male

**Age: **6 months

**Symptoms/Injuries:**

Decay of power generating ectoplasmic cores

Extreme dehydration

Perforation of cellular membranes

Degraded nucleus integrity

Complete loss of intercellular cohesion

**Conclusion:**

Decay of ectoplasmic cores resulted in massive cellular damage, before eventually tearing them apart entirely as the volatile ectoplasm lost its cohesiveness.

Cause Unknown.

* * *

******07/03/2005**

**Audio Transcript, ****_Vladimir Masters _**

Despite substantial variation in the conditions used to stimulate the formation of a Primary Core, Clones 5 through 13 have all succumbed to Destabilisation, as I have termed it.

This has become a time consuming process, and it has told me nothing about the cause.

I suspect that it is caused by a flaw in the Core Formation process, but I have no way of determining exactly what that flaw may be.

It may also be a result of the cloning process, or some instability introduced by repurposing mature, differentiated cells. If so, then I would have to abandon the cloning approach, which would defeat my purpose of producing a clone of Daniel to become a son and heir for myself.

I will come back to this quandary; I cannot think clearly after another abject failure.

* * *

******07/12/2005**

**A****udio Transcript, ****_Vladimir Masters_**

I have decided that a new approach should be trialled.

Theoretically, it should be possible to create an individual that possesses a near-identical genome to Daniel by combining portions of his genetic material with an Egg from a carefully selected donor who has a similar phenotype.

Obviously Maddie would be ideal, but I cannot find any evidence that she has stored any eggs that I could gain access to, and the possibility of some unintended genetic damage resulting from crossing a Parent with the F1 generation cannot be discounted either.

No, it seems I will have to find another unwitting donor, and that will give me the time to consider and rectify possible flaws that may occur as the program progresses.

I will also continue with the standard clones, in an effort to determine precisely what is causing their susceptibility to Destabilisation and if there are any possible ways to rectify it.

* * *

**[AN: I'd love to know what you readers think of this concept so far. It's a different writing style than I've tried before so feedback would be amazing.**

**As for 'The Events that Shape Us', I will post the epilogue I have planned at some point, after I have finished this piece (it shouldn't go for more than 5 chapters), as there are some things about Danielle that I want to explain before I get to it in the narrative pieces.**

**Also, please ask any questions you have and tell me if you found anything confusing.**

**Thanks again /AN]**


	2. Genesis

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: First off; five reviews in twelve hours, that's definitely a new record (for me). It's great to know that you guys are interested in the concept so far.**

**Second; yes I've changed my name. I never was a fan of having a screen name with a string of numbers after it, and then I remembered I had come up with this one a while ago and never used it again. I thought it was quite fitting.**

**And thirdly; I've played around with the dates in the first chapter, so if you care about that sort of stuff, go ahead and check out the slightly altered timeline.**

**Enough rambling, here's the next chapter; I hope you find it equally as interesting as its predecessor./AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 2: Genesis**

* * *

******08/23/2005**

**Audio Transcript****, ****_Vladimir Masters_**

At last I have found a suitable 'mother' for my experiment, and the irony is simply delicious.

By some remarkable twist of Fate, young Ms Manson has had some of her eggs cryogenically stored at Amity General, which I just so happen to own.

It seems Pamela suffered from an unfortunate defect in her Fallopian Tubes that only became apparent after her pregnancy with Samantha. It certainly explains why they never had another child; a fact I had always considered odd, considering how status conscious they always appear when they bore me at society events.

It seems they did not wish to risk a similar occurrence with young Samantha, should she ever get married.

To that end, they scheduled an operation to harvest and store some of her eggs, in the event that she was unable to conceive naturally.

Naturally, this was not told to Samantha, who was twelve at the time, and was done under the pre-text of removing her appendix.

This is truly a windfall, as both Daniel and Samantha share a remarkably similar Phenotype, both having strong Gaelic heritage on their maternal sides and Germanic heritage on their paternal sides, and their overall genotypes are probably even closer than their phenotypes would indicate. In addition, the eggs have been in storage for less than five years, which should increase their viability.

Really, the fact that young Daniel seems to have some bizarre, quasi-romantic relationship with the girl only makes it that much more fitting that she should become the donor for my experiments.

It's almost a pity that I will have to terminate the majority of them.

* * *

******08/23/2005**

**Ova Storage Documentation:**

**Name: **Manson, Samantha Ruth

**Date Collected: **11/04/2000

**Institution Responsible: **Amity Park General Hospital

**Surgeon Presiding: **Dr Herbert, Timothy Jones

**No. of Ova Collected: **Seventy-Five

**Permission Granted By: **Manson, Jeremy Thomas and Manson, Pamela Michelle

**Authorisation for Storage: ***Signed 'T. Herbert'*

* * *

******10/06/2005**

**Audio Transcript, ****_Vladimir Masters_**

The first batch of fertilised eggs were all failures, either failing to divide once they became a Zygote or possessing an unsatisfactory genotype.

I have purged the growth tanks and am prepping the next sequence of fifteen eggs.

It is a pity that genetic splicing is so hit-and-miss but my first attempts have helped me narrow the selection of enzymes that could achieve the desired results.

Of course, this endeavour is not helped by the variable nature of the genotype within the gametic Ova, but at least the ideal genetic sequence that I have developed from Daniel can be recreated easily with Polymerase Chain Reactions, though I will need to restart the process in the near future if I am to continue this line of experimentation.

Of course, extracting and inserting a micro-core from one of his cells into the first stage zygote is more difficult, but the process is becoming rather mundane after the number of times I have successfully achieved exactly that.

* * *

******11/09/2005**

**Audio Transcript, ****_Vladimir Masters_**

It seems my second attempt has gifted me with a worthwhile subject.

The combined genotype is remarkably similar to Daniel's, which isn't surprising as I used a higher proportion of his genetic material in this particular attempt, and at one month the embryo shows no adverse reactions to the nutrient and hormone cocktail used in the pseudo-gestation process to accelerate the time between my attempts.

There is one minor issue, however; this one turned out to be female.

While this is unfortunate and obviously unsatisfactory for my ultimate goal, it is mostly irrelevant in terms of this subject's role. It (or she, rather), only needs to be close enough genetically to Daniel to see if the Destabilisation is caused by a defect in the Cloning Process or the Core Formation Process.

Gender should have limited to no observable impact in terms of this goal and I do not wish to waste more time hoping to produce another sufficiently close match, so this one will have to suffice.

I will need to alter the hormone mix slightly to account for the different physiology between the genders, but otherwise everything is in place.

The remaining results from batch two have been terminated.

* * *

******11/09/2005**

**Subject Summary Document:**

**Batch Number: **Two

**Egg Number: **Seven

**Designation: **O/HF 2-07

**Date of Conception:** 10/08/2005

**Primary DNA Source: **Fenton, Daniel J.

**Egg and Secondary DNA Source:** Manson, Samantha R.

**Source Percentages**: 68% Primary, 32% Secondary

* * *

******12/12/2005**

**Audio Transcript, ****_Vladimir Masters_**

An update on Subject 27; two months in and pre-natal development is nearly concluded.

While this is rapid by conventional standards, it is strangely delayed compared to the pure clones, possibly as a result of the lack of telomere markers in 27's cells.

Other than this discrepancy, development is progressing normally and earlier concerns I had about 27's capacity to produce ectoplasmic micro-cores appear to have been unfounded.

My attempts with the standard clones are continuing to fail, regardless of how I manipulate the environment during Core Formation. This leads me to believe that the Destabilisation is caused by a fault in the cloning process, but the results of what occurs with Subject 27 will be the true test.

In the mean time, I have altered the cloning process slightly to accelerate the rate at which I can produce these clones. They are worthless as possible sons until I have had the chance to solve the Destabilisation issue, but they will provide a useful base to study the condition's physiological effects.

The changes will result in a higher rate of mutation and genetic degradation, but they won't live long enough for it to matter anyway.

* * *

**[AN: And there you have it, my theory on exactly how Vlad came in to possession of Sam's eggs. I'd love to know what you think about it, whether it's too far fetched or not, etc.**

**And points to anyone who can guess the reference that is Sam's middle name.**

**I've heard/seen Lilith used a lot, but I can't find any canon confirmation for that being her name (please do correct me if I'm wrong however), so I decided to come up with my own, and I think it's quite fitting.**

**I feel this is a quite dark chapter, but it's only going to get worse really; there is simply no way in which anything about Vlad's cloning operation could ever be considered cheery...**

**Please do ask if you have any questions or queries about stuff in the story, it's what I'm here for. The amount of Biology jargon is only going to increase.**

**Also, if you have any questions relating to things you believe are unresolved about Danielle's existence or her portrayal in my other stories, then ****_please_ tell me as I'd love to discuss them or attempt to answer them, if I don't already plan to do so.**

**Thanks again, and I hope you enjoyed the chapter. /AN]**


	3. Development

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: I've taken a bit of artistic license with the science of this chapter, mainly because the human Endocrine System is not an area of specialty for me and I don't particularly feel like doing a couple of weeks of research to work out exactly how Vlad would go about this.**

**So instead I've generalised it.**

**I've tried to keep it as accurate as possible but beyond the names and broad functions of the Hormones, everything else is pretty much made up or summarised heavily.**

**I've also gone back and made some edits to Ch2. Nothing major, but I just figured I'd let y'all know./AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 3: Development**

* * *

******01/06/2006**

**Audio Transcript, ****_Vladimir Masters_**

I have just completed a procedure to hopefully eliminate an important portion of the Endocrine System from Subject 27.

This was necessary in order to avoid complications arising in the future as the body's natural homeostatic counter-measures attempt to cancel out the influx of growth hormones in the Gestation tank.

A Gamma Knife was used kill numerous cells in the Posterior of the Pituitary Gland, hopefully restricting its function in producing growth hormone inhibitors such as Somatostatin. It also damages the brains ability to instigate and regulate the onset of puberty, so that must be observed closely.

I will know if the operation was successful in a month or so.

* * *

******02/17/2006**

**Audio Transcript, ****_Vladimir Masters_**

Four months in and Subject 27 is progressing well. Physiological development is equivalent to that of a six year old child, which, while still slow compared to the other clones, is faster than early growth rates had indicated.

Equally as important, the subject shows high levels of neural activity, certainly higher than any of the clones did at this point in their development cycle. As a result, I have initiated the imprinting sequence two weeks ahead of schedule and so far the results are promising.

As expected, the attempts to limit the Subject's ability to produce and regulate the hormones specifically related to growth and maturation have been successful. The regions of the Pituitary Gland that produce those hormones have been effectively neutralised.

Of course, this means that the process of puberty must be manually induced, which requires careful balancing of hormonal percentages and saturations; many of the first clones that reached this stage perished as I attempted to find the right method.

But they were all male, so Subject 27 will present her own challenges in this respect, but I have confidence that the processes should be reasonably similar.

If development continues along the plotted course, then I will begin the new hormone treatment in 24 days time.

* * *

******03/16/2006**

**Hormone Treatment Plan:**

**Subject Designation: **O/HF 2-07

**Date of Commencement: **03/16/2006

**Date of Completion:** To Be Determined

**Hormone:** Somatotropin

**Recommended Dosage:** 35ppm

**Regularity of Administration: **Daily

**Function:** General Growth Hormone, responsible for most of the growth over an individual's lifetime.

**Hormone: **Oestrogen

**Dosage: **19ppm

**Regularity of Administration: **Twice Weekly

**Function:** Primarily responsible for the development and regulation of female reproductive organs.

**Hormone:** Progestrogen

**Recommended Dosage:** 12ppm

**Regularity of Administration: **Twice Weekly

**Function:** A counterpart to Oestrogen, fulfilling the same broad roles.

**Hormone:** Testosterone

**Recommended Dosage: **2ppm

**Regularity of Administration:** Fortnightly

**Function: **An Androgenic steroid, largely responsible for building muscle mass.

* * *

******05/02/2006**

**A****udio Transcript, ****_Vladimir Masters_**

Subject 27 is approaching a point of development where decanting her and beginning my experiments is quite viable, though she is still smaller and less developed than the clones generally are at this point.

This may be due to the imperfect hormone regime or a result of her unique heritage, the only way to determine which would be with more experiments and it is, in the end, an irrelevant question for the moment.

Regardless of the reason, her growth is substandard but sufficient, barely, for my purposes.

I will decide on this at another time, the next set of clones requires my attention…

* * *

**[AN: And there you are, the next chapter will have much more Danielle in it, mainly because she'll finally be conscious... not that that's a good thing in this situation...**

**Still no guesses for why I chose Ruth for Sam's middle name?**

**As always, please feel free to ask me questions, I'll do whatever I can to help clarify.**

**Thanks for reading! /AN]**


	4. Surprises

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: First, let me apologise for the week long delay, it was not my intention but other things came up. **

**I had to triage my stories, but not to fear, it was in order to give me more time for my DP ones, including this one.**

**I hope the next update will be quicker, but I will not make promises that I can't keep.**

**Until then, here's the next chapter./AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 4: Surprises**

* * *

******05/15/2006**

**Security Footage, ****Camera 3 – Main Laboratory, Angle 2:**

*View of main Laboratory with a large growth tank set on the far wall, slowly draining of fluids*

Computer System: _"__Decanting Process complete, specimen is now ready for removal."_

Vlad: "Excellent, release the locks and open the tank."

Computer System: _"__Releasing Locks."_

*Audible hiss of a pneumatic seal being broken*

Computer System:_ "__The chamber is now open and the specimen awaits retrieval."_

*Vlad, as Plasmius, approaches the tank with a gurney and appraises the subject contained inside*

Vlad: "Fascinating, this one should do nicely."

*Vlad removes the young girl from the container and straps her onto the gurney, then places a sheet over her exposed body. The gurney is then rolled of screen*

* * *

******05/15/2006**

**Audio Transcript, ****_Vladimir Masters_**

I have removed Subject 27 from the growth chamber. Preliminary physical examinations show no signs of growth abnormalities or cell degradation; a good result considering this was the first subject developed completed with this new method.

When she wakes up I will complete the cognitive tests and check organ functionality.

If all is well, then 27 will undergo Core Formation within the week.

I eagerly await the results of that experiment.

* * *

******05/16/2006**

**Audio Transcript, ****_Vladimir Masters_**

Much to my irritation, it seems that 27's cognisance has developed independently from the indoctrination program.

Rather than simply knowing what was imprinted into her mind subliminally during her growth like the other Clones, she has a unique, and annoyingly inquiring, mind. She has been asking questions incessantly, the first of which was what her name was after I introduced myself; I have told her that her name is Danielle, for lack of a better option available to me at the time.

Her speech patterns are well developed and her knowledge of the imprinted information is exceptional, possessing near complete re-call. Clearly these are desirable traits compared to the traditional clones, whose memory retention is sub-par, to say the least.

Unfortunately, it seems to come at the price of incessant curiosity and an inability to follow simple instructions!

*Deep breath, followed by a sigh*

I as of now cannot determine whether this is a by-product of her unique genesis or the result of starting the education and indoctrination sessions earlier than normal, but it does warrant further investigation, as if I could harness such enhanced intelligence for my final project, it would be a substantial improvement over previous attempts.

*Crashing sound of something hitting the floor*

(Unknown speaker [ID'd as Danielle]): _Who ya talking to? Can I talk to them? Or are you just talking to yourself?_

*Loud sigh*

(Vlad): It is none of your concern Danielle, I have already told you to stay on your bed until I tell you otherwise.

(Danielle): _But I am still on my bed, see? Wheeeeeee!_

*Rattling sound, presumably the gurney rolling past*

* * *

******05/16/2006**

**Cognitive Testing Results:**

**Designation:** O/HF 2-07

**Date: **05/16/2006

**Sex: **Female

**Age: **7 months

**Score:** 208 out of 220

**Avg. Mark:** 163 out of 220

**Estimated IQ:** 135

* * *

******05/16/2006**

**Security Footage, ****Camera 5 – Medical Station, Angle 1:**

*Danielle, now clothed in a hospital robe, is sitting on the gurney, legs swinging aimlessly over the edge as she looks around the room. Vlad enters the room*

Vlad: "Good, you are awake. My name is Vladimir Masters, but you may refer to me as Sir, Master, or Father, if you must. Now you-"

Danielle: "Cool, what's my name then?"

Vlad: "Your name is 27, and-"

Danielle: "That's not a name, silly! That's a number! So what's my name? Or, *leans in and whispers* is it a secret?"

Vlad: *Sighs irritably* "Very well, your name is… Danielle, yes, your name is Danielle."

Danielle: "Awesome! Can I just shorten that to Dani? With an i? Danielle just seems soooo long."

Vlad: "No, you cannot. Besides, it has the same number of syllables."

Danielle: "Yeah, but it _sounds_ shorter."

Vlad: "Your name is Danielle, that is the end of the matter. Now I need you to complete the questions on this paper. I will return in an hour to retrieve the paper and bring you some food. I expect the paper to be completed, and you are not to leave your bed."

Danielle: "Sure!"

*Vlad nods and walks off screen*

* * *

**[AN: So there's your first taste of Dani, what did you think? I'm working on the assumption that Vlad treated her reasonably well considering she was quite willing to work with him until she found out the truth, so there won't be any abuse or violence, just Vlad's usual callousness and lack of empathy.**

**I hope you enjoyed it, and any feedback would be great./AN]**


	5. Betrayal

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: Well, I managed to so slightly better than a week, barely****.**

**game that we get to see in the show, hence the title. There are still some more chapters to come, so I guess my assertion that this "shouldn't go for more than 5 chapters" in the AN at the end of the first chapter was a bit erroneous, huh?**

**Oh well, enjoy! /AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 5: Betrayal**

* * *

******05/20/2006**

**Audio Transcript, ****_Vladimir Masters_**

Subject 27 underwent the Core Formation process an hour ago and I am now awaiting the results.

On the surface, everything appears to have run smoothly. The settings used were the ones that had given me the most successful results previously, the clones lasting for almost 4 hours in the training course before succumbing to Destabilisation.

The scan results and biopsy reports are being compiled as I speak and should be ready soon. 27 is sleeping currently, in preparation for her attempt at the training course tomorrow.

* * *

**********05/20/2006**

**C****ore Formation Preliminary Report:**

**Designation:** O/HF 2-07

**Date: **05/20/2006

**Sex: **Female

**Age: **7 months

**Scan Summary:** No abnormalities detected, standard levels of background ectoplasmic energy being produced. The Core formation process appears to be complete and stable.

**Biopsy Summary:** Intra-cellular Micro-cores functioning at substantially higher levels than before undergoing Core Formation. They are now producing energy at rates concurrent with observed levels in other Halfas.

* * *

**********05/21/2006**

**Security Footage, ****Camera 8 – Training Room:**

*Danielle enters the training Room*

Vlad:_ "__Ah Danielle, thank you for showing up. I need to test your new Core, to see if it is working properly. Now transform."_

*Danielle transforms quickly and appears excited at her new appearance*

Vlad: _"__Excellent. Now Danielle, I'm going to run you through some test to try out the various powers you should have. I trust you will know how to use them, based on your test results. Try invisibility."_

*Danielle blinks out of the visual spectrum*

Vlad: _"__Very good, now let's try intangibility."_

*Danielle reappears, and shies away immediately when a baseball comes flying towards her. The baseball, however, passes right through her*

Vlad: _"__Alright, now hit the targets as they appear."_

*Three targets drop down from the ceiling and Danielle hits all three with ecto-blasts, obliterating them.*

Vlad: _"__Good. Now I want you to try flight."_

*Danielle floats upwards and starts giggling to herself, doing loops and rolls*

Vlad: _"__This is not the time for fun and games! As long as you follow my instructions and perform adequately, this test will be over as soon as possible. This next test will let me monitor your evasive capabilities."_

*An automated ecto-gun begins firing rounds at Danielle. She dodges all five rounds, though only just*

Vlad: _"__Excellent work. Now, on to some more difficult tests…"_

*Video skipped ahead 5 hours. Danielle is noticeably weary and burns and faint traces of blood are visible where ecto-weaponry has impacted her, though the wounds are minor at worst*

Vlad: _"__This is the final test Danielle, you have done very well so far. I need to see you use all of your powers in combination, so you have full discretion to complete this test as you see fit. You must hit all of the targets, dodge as much fire as possible, and complete the obstacle course."_

*Danielle beings the course, using invisibility to bypass turrets, intangibility to avoid projectiles and ecto-shields to protect her from incoming fire. She destroys the targets with precision and a variety of techniques. She takes seven hits by the end of the 15 minute course.*

Vlad: _"__Well done Danielle, well done indeed. Go get cleaned up and Dinner will be ready shortly. I'm sure there will be some special desert given your performance."_

*Despite her obvious injuries, Danielle smiles brightly and flies out of the room.*

* * *

**********05/21/2006**

**Audio Transcript, ****_Vladimir Masters_**

Today contained some _very_ exciting developments for my project.

Subject 27 completed the Training Course! All 6 hours, with no signs of Destabilisation. Equally as interesting, her control and finesse were far greater than any of the clones with the same level of experience. Still not close to myself or even Daniel, but impressive none the less.

This result implies that there is a flaw in the cloning process, something that makes the resulting ectoplasmic cores unsustainable. It will be difficult to determine exactly where the problem lies, but this experiment has helped substantially narrow the possibilities down.

It has also shed light on the potential this gamete based system has, particularly if the heightened intelligence and control are a consistent result and not a one-of only seen in 27.

I will run one more test series in two days time to gather a final set of data, then I will terminate and begin the next set.

* * *

**[AN: So, as previously stated, there are more chapters to come, at least two, maybe more depending on how they balloon out. The final will be an appendix-like piece by Jack and Maddie, detailing the abnormalities growing up that Danielle can expect to face as a result of Vlad's methods.**

**So until then, I hope you've enjoyed the latest chapter. /AN]**


	6. Manipulation

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: I apologise for the week-long delay, I experienced some technical difficulties that kept me away, but here is the next chapter.****/AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 6: Manipulation**

* * *

******05/23/2006**

**Audio Transcript, ****_Vladimir Masters_**

It seems my willingness to discard 27 may have been somewhat hasty, as the last set of tests showed the beginnings of Destabilisation setting in. It's slight, and not nearly as rapid as seen in the clones, but it does raise some interesting questions.

It's possible that there is a flaw in the Core Formation process which is triggering this effect, but that it interacts with something on the genetic level, which would explain why 27 has been rather more stable, as she is far more genetically stable than any of the clones.

I will observe her eventual degradation and see what information I can gather from it, as in all other cases, the Destabilisation happened over far too small a period of time to effectively monitor.

It seems this flaw of hers has just extended her usefulness to me, how ironic.

* * *

******05/23/2006**

**Core Formation Follow-Up Report:**

**Designation:** O/HF 2-07

**Date: **05/23/2006

**Sex: **Female

**Age: **7 months

**Scan Summary:** Possible anomaly detected, standard levels of background ectoplasmic energy being produced, but in an erratic pattern. The Primary Core is stable for the time being, but energy production is rising and falling at seemingly at random.

**Biopsy Summary:** Intra-cellular Micro-cores continuing to function, but variance detected, with slight shifts in the normally uniform appearance of the cores. Energy production is fluctuating slightly, similar to what is currently being seen in the Primary Core.

* * *

******05/31/2006**

**Audio Transcript, ****_Vladimir Masters_**

Subject 27 continues to progress well, she seems unaware or her cells beginning to fail her.

This is not surprising, considering that, while consistent, the rate of degradation is very slow currently; often below one hundredth of a percent of overall output per day.

At a rate like that, it could be decades before I would start to see results; and that is an unacceptable outcome.

Thankfully, it appears that rate of onset increases whenever the cores are exposed to high levels of ectoplasmic energy, such as the use of her ghost powers, or being impacted by an ecto-weapon.

I have increased her training regime as a result and I expect to see a far more reasonable rate of decay within a fortnight.

I am also making progress on determining what it is about the genetic structure of 27 that has made so comparatively resilient to the effects of Destabilisation.

* * *

******06/09/2006**

**Audio Transcript, ****_Vladimir Masters_**

Finally, I have it!

I spent far too much time looking for a hereditary genetic explanation when I should have been focusing on the physical properties of the genetic material itself.

It seems as though the DNA stored in the Nucleus, once exposed to ectoplasm, polarises itself into a specific state, much like iron crystals aligning themselves with a magnetic field. The cell begins to reject any ectoplasm of a foreign polarity, eventually causing the Cores inside the cells to Destabilise.

It also seems as though this polarisation is passed on during replication once a cell has differentiated, which would explain why my PCR versions still retained this distinct signature.

It appears the only way to avoid this would be to ensure the cores form in exactly the same polarity as the original exposure, but seeing as how ectoplasm is a volatile, extra-dimensional material with near limitless ways to align itself, this would prove to be almost impossible.

It also explains Subject 27's uniqueness in this area.

The reason she has been so resistant to Destabilisation so far is that she is not made up entirely of Daniel's genetics, and the natural recombination of the two sources produced new chains that broke the present polarisation.

Of course, portions of it still exist, enough to begin rejection and ensure that it is completed, but at a substantially slower rate than in the clones.

And that showed me the solution, all I needed was a pure, undifferentiated cell from Daniel, and I could successfully clone him. That means I need to acquire a stem-cell from him, not an easy task to say the least, but it vindicates my work and gives me a way forward.

Once again, 27's success has made her obsolete.

* * *

******09/22/2006**

**Audio Transcript, ****_Vladimir Masters_**

Damn these Clones!

I have sent nearly a dozen of them after Daniel so far, in an attempt to capture him so I can extract the necessary cells, but telemetry indicates they barely reach Casper High before they are eradicated; they simply can't stand up in a fight against someone as powerful as Daniel and it is far too risky for me to go myself.

Of course, Subject 27 stands a much better chance, due to her far more stable state. I also imagine Daniel's innate empathy will work against him in this case; he has shown a remarkable reluctance to injure Ms Gray and the destruction of the current clones is an unintended side-effect of their instability rather than an active attempt on his part.

I will send 27 after him in a couple of days if the next set of clones also fails, which is rather likely, unfortunately.

* * *

**[AN: And there you have it. I've only got two more chapters planned after this, so it's nearly done. With any luck, I should be done within a week, but I can't say that for certain.**

**Thanks again for taking the time to read./AN]**


	7. Self-Realisation

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: Once again, I apologise for the delay, this time it was the flu that impacted my writing schedule.**

**But to make it up to you, here is the longest chapter yet and the final Vlad-based chapter for the story!**

**This one basically takes place as an altered version of the episode "Kindred Spirits", and it effectively leads in to my other Danielle-centric fic 'The Events That Shape us'/AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 7: Self-Realisation**

* * *

**__****06/27/2006**

**Audio Transcript, ****_Vladimir Masters_**

I will be sending Subject 27 to retrieve Daniel in less than a day.

It is a calculated risk, as she is a valuable specimen, but the benefits far outweigh the loss of a single, albeit useful, experiment.

Of course, if she fails, then my only remaining course of action would be to become involved myself and kidnap one or more of Daniel's loved ones, Samantha if no one else, and force him to cooperate.

That plan of action runs the risk of unleashing his dangerously erratic anger, however, and with such powerful emotions fuelling his powers, he is a substantial threat; still easily manipulated, but extremely dangerous.

I would prefer to avoid such a risky sequence of actions.

* * *

******06/28/2006**

**Audio Transcript, ****_Vladimir Masters_**

Telemetry data shows that she has reached the core of Amity Park, which is substantially further than any of the other clones got before being destroyed, but she has been largely stationary for quite some time.

It is odd, she hasn't destabilised, nor has she been captured in one of those infernal Thermoses, and she certainly isn't fighting; it's almost as though she is waiting… or talking?

Perhaps Daniel's empathy _has_ gotten the best of him once again…

* * *

******06/28/2006**

**Audio Transcript, ****_Vladimir Masters_**

Ah Daniel, always so predictably easy to manipulate. I should have known from the beginning that he have would responded better to his own daughter than to a horde of degenerate clones.

Of course, neither of them have any idea that they're related in such a way; a piece of information that I have no intent of sharing with them, either. If either of them were to find out the truth, the resulting fallout would be inconvenient… and expensive.

Still, Subject 27 has made it almost laughably easy to contain Daniel.

He won't attack her, while she is quite aggressively protective of me and won't allow him to make any move that I haven't allowed. As such, he really has very little choice other than gravely injuring the young girl or submitting himself to my will. And of course, I need only threaten _her_ life, and poor Daniel wouldn't dare to even consider attacking me.

His is obviously only a temporary state, there are far too many variables and long-term issues to account for if I were to try and use her as leverage for forcing him into my service, but it should prove to be sufficient for gaining the stem-cell samples that I need to perfect my cloning process.

Now to finish my preparation for the operation.

* * *

******05/16/2006**

**Security Footage, ****Camera 5 – Medical Station, Angle 1:**

*Danny is strapped down on a gurney, in full ghost-proof restraints. He is struggling but unable to move. Danielle floats in ghost-form near the gurney, ready to attack if necessary*

Danny: ""

Vlad: ""

Danny: "Danielle, please, you have to listen to me! Vlad's a psycho, he's just using you! If he gets whatever it is he wants from me, he'll kill you!"

Danielle: "Shut-up! You're lying! He's my father, he won't hurt me. And you're the one that killed all the others, so why should I believe you?"

Danny: "I don't really have time to explain my history with the Fruitloop over there, but I swear, he's the bad guy! I didn't want to destroy the other… things. They were practically falling apart when I found them and even the slightest hit, and they would disintegrate. I tried to help them, but there was nothing I could do! Why can't you-"

*Danny is cut off of Vlad enters the room (as Plasmius), carrying a tray of biopsy equipment*

Vlad: "Ah Daniel, trying to turn my own daughter against me? How very pathetic. Danielle, I trust you ignored his ravings completely?"

Danielle: "Yep! Just like you said."

Vlad: "Good girl. Go and get yourself a treat, and don't come back for half-an-hour or so. I wouldn't want your young mind to be impacted by seeing a surgery at your age."

*Danielle nods eagerly and flies out of the room*

Vlad: "Don't you find it amusing that your own clone prefers to listen to me, rather than you?"

*Vlad cuts a small square of fabric out of Danny's jeans, over his femur and swabs disinfectant over the exposed skin*

Danny: "No, not really. What did you do to her anyway? I'm guessing you brainwashed her, like the others?"

*Neither party sees Danielle silently return into the room. She looks like she's about to speak, but stops when Vlad replies*

Vlad: "Quite the opposite, in fact. She is the only one in which the pre-conditioning failed. No Daniel, her obedience is simply the result of some kind words and the barest hints of affection. Children do so crave it at that age, and they will go to great lengths to obtain it."

Danny: "So what will happen to her once you've finished with me."

Vlad: "The very same thing that happened to all of her predecessors. She will be completely obsolete once I have a culture of your stem cells. I think there is something poetic in her greatest accomplishment causing her own redundancy."

Danny: "You're going to kill her, aren't you?"

*Vlad prepares a large biopsy needle and positions it in its clamp over the previously prepared area*

Vlad: "My my, so sentimental, aren't we? I terminate them; to say that I kill them implies that they were alive in the first place. They only ever had one purpose, to exist as experiments until they were no longer required. They were no different to a tissue sample, simply more complete"

Danny: "How- how can you just treat them like that? Don't you care in the slightest!? She's willing to die to protect you, and you're just going to throw her away."

Vlad: "Hardly, she is still a useful data point for my study of Destabilisation. I will simply accelerate the process. Now, are you finished asking your self-evident questions so I may continue with my task?"

*Vlad turns around to take something off the tray, but spots Danielle hovering near the doorway*

Vlad: "Danielle!? What are you doing here? I thought I told yo-"

*Loss of camera feed, both video and audio*

* * *

******06/29/2006**

**Audio Transcript, ****_Vladimir Masters_**

Confound it all! The blasted girl overheard me and freed Daniel, before I could begin the operation.

They then annihilated my facility and fled back to Amity Park.

It is more of an inconvenience than a total loss; my back-up retained all of the data and notes of my work up to this point and the loss of equipment is negligible considering I have three other facilities and the equipment is all of my own design.

The real issue is that I cannot continue my work until I can capture Daniel again. Danielle will not allow herself to be used in such a fashion again and my sources indicate she fled Amity Park and has gone into hiding anyway, and Skulker has proven to be completely outclassed by Daniel on an uncountable number of occasions.

That really just leaves Ms Gray, though she is still a good deal away from being able to successfully capture Daniel. But in time, she may be my most useful pawn…

* * *

**[AN: And there you have it.**

**The next and final chapter will be an addendum by Jack and Maddie, adding their own study into Danielle's unique biology and its potential effects on her future growth. It will also be followed soon after (read: a day at most if I don't get to impatient) by the epilogue for 'The Events That Shape Us', as it will draw on some of the points raised in the final chapter.**

**Thanks again for reading and I hope you have enjoyed the story! /AN]**


	8. Future Concerns

**Disclaimer:** I do not own 'Danny Phantom' or any of the characters, concepts etc. Those are owned by Butch Hartman/Nickelodeon, I believe. I make no claim to anything in this story, it is a perspective with hypothetical scenarios added in.

**[AN: And here you are, the final chapter in this little story. I won't take up any more space up here, so I hope you enjoy!****/AN]**

* * *

**When is a Clone not a Clone?**

**- The Danielle Codex-**

**Part 8: Future Concerns**

* * *

**Addendum by Maddie Fenton**

I wish I could say the horrors and suffering Vlad inflicted on Danielle were now at an end, but our own research leads us (myself and Jack) to believe that the damage Vlad's methods did to her will continue to affect her for the rest of her life.

What follows is a list of likely side-effects and concerns that we expect to see, or have already started seeing in her as she matures:

* * *

**Growth:**

One of the most noticeable things about Danielle is her small stature. Despite development of certain puberty-related traits being equivalent to an early teen or late pre-teen, her overall size is more consistent with prepubescent child. We believe that this is a result of the damage Vlad caused to her endocrine system in an effort to manipulate her hormone production.

It seems as though she has failed to undergo the standard growth-spurts associated with entering puberty. Danny was certainly much taller by the time he reached the same equivalent point of development, and I can't say I remember Sam ever being so small either, so it is almost certainly not a genetic factor.

The main evidence, though, is that in the year that she has been with us, she has grown less than half an inch. Telomere analysis suggests she should be approximately thirteen years old, and about two years into puberty by now, so such a lack of growth is all but unheard of.

We have started her on a hormone treatment plan to attempt to make up for her damaged system, but she will never undergo the normal growth-spurts, as it is simply too dangerous to try and force such effects. Instead, she will most likely grow at a more consistent rate over the next five or so years, but we won't really know for a while yet.

* * *

**Core Stability:**

Unfortunately, we really don't know enough about the formation and stabilisation of ghost cores to really determine how stable Danielle actually is at the moment, or what effects Vlad's artificial attempts could have had on her ectoplasmic physiology. This leaves her in a potentially dangerous situation, as her destabilisation may set in again without warning, or it may never be an issue ever again.

It seems that the introduction of a more energetic ectoplasm isotope was all that was required to stabilise the core initially (which makes sense as the Ghost Zone is not made up of a uniform type of ectoplasm) but we simply can't know if it will stay that way. Vlad's notes suggest she appeared stable until she was hit with ectoplasmic energy, at which point her cores slowly began to weaken and the possibility remains that this may occur again. We will continue to monitor her for any sign of instability and we're also continuing our research into possible solutions should the 'Ecto-Perfecto' method prove to be ineffective.

* * *

**Psychological Trauma:**

It shouldn't come as a surprise to anyone who knows her story, but we have serious concerns about Danielle's mental health after everything that she has been through.

Danny has told us that she still suffers Nightmares at least once a week, and quite possibly more. The regularity has certainly decreased if that is the case, but the severity hasn't. I can see it in her eyes when I see her in the morning after she's had one, the fear is still present until Danny and Sam have the chance to calm her down and reassure her.

Jazz is also gravely concerned about her self-image. She says that she's at risk of feeling as though she has no intrinsic worth and that she will strive to prove herself, most likely through her ghost hunting, driving her to take and on more and more dangerous foes. She also thinks this was a motivating factor for Danny early on, but he moved past it quite quickly.

It's one of the reasons I'm so glad that Sam's around. She's been a fantastic mother to the poor girl as well as being the perfect role-model for her; independent, self-assured without being demeaning or spiteful towards others, and a passionate, kind-hearted young woman.

Danielle also craves physical contact, seeking it whenever possible, as long as it is with someone she is comfortable around. It's not much of a surprise, as Vlad could never be considered to be particularly affectionate, but it does mean that she is at risk of people taking advantage of her as she grows up. Danny's protective nature helps a lot in that respect, but he won't always be able to protect her, so again, Sam and Jazz have been fantastic influences for her.

* * *

**Rapid Aging Effects:**

This is one of our greatest concerns; we really have no idea how Danielle's rapid development will affect her as she grows up. A telomeric analysis indicates that her cells have undergone far more growth in a short space of time than they should have, nearly ten times more, but we have no way to determine how that could change anything as she develops.

Our main concern is that it will lead to permanent damage at a genetic level, which could result in a number of very serious side-effects, including cancer.

This concern is compounded by the still unknown effects of the rapid, ectoplasm powered healing that both Danny and Danielle exhibit. We still can't get a solid result on whether or not it has any impact on cellular degradation and telomere effects or not.

And that really is the main problem, we just don't know, we can only wait and see and hope.

* * *

**Sterility:**

This is more of an insult than and injury, but it is no less of a concern for us. Danielle might not be at an age where raising her own family has even crossed her mind (nor will she be for years to come), but we have considered it.

There is no conclusive evidence that she is infertile, as we don't want to subject the poor girl to any more invasive procedures, but it is still a serious concern. Her rapidly forced development, severely damaged endocrine system and artificially manipulated genetic makeup is not conducive to fertility, but it's still all just speculation.

We just hope for her sake that it won't be Vlad's final insult to her.

* * *

We have provided Danny and Sam with a… summarised version of this booklet, all the important parts and the information they need to know. We believed that they didn't need to see everything that Vlad did to their little girl.

Tucker and Jazz agreed.

In time, perhaps we might show them everything. One day, we might even show Danielle, if she ever truly wants to know everything that went into her creation. But for the moment, they don't need to know.

* * *

**[AN: And there you have it, the completion of the Danielle Codex. Thank you to those who have read it and triple thank you to those who have come back chapter after chapter to read and give me their thoughts and feedback; it's a massive encouragement for me personally.**

**Really, I just hope you enjoyed the story, if you can call it that.**

**As with all my other stories, if you for one reason or another wish to use and idea that I've come up with or a bit of background from this one, feel free and just let me know, because I'd love to check it out!**

**And as usual, all feedback is gratefully received, and if you have any questions, I'll do my best to answer them.**

**Thanks for checking this story out and keep an eye out for the epilogue to 'The Events That Shape Us' that I'm hoping to have up very soon.**

**Thanks again! /AN]**


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